spatialdata
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scverse
An open and interoperable data framework for spatial omics data
Made get_values work for tables that annotate points Added a check for index dtypes in the element and the table annotating the element.
Across the repos we use sometimes `coordinate_system`, `to_coordinate_system` and `target_coordinate_system`, `coordinate_systems`. We should replace all the occurrences with `coordinate_system`.
@LucaMarconato has observed that load lots (1E6) points is slow. Thus, we should discuss lazy loading and using some sort of spatial index for query. A few points: - we...
When we read polygons/multipolygons from disk we use the ragged array representation. I have just noticed that the `geometry` parameter is a single value and not a vector. We need...
Currently we need to do `Image2DModel().validate()`, while all the parser and the non-raster validation methods are accessible as class methods: `Image2DModel.parse()`. We should fix this.
I suspect that we are not enforcing that the dtype for labels should be an integer. We do the check when we validate the target of a table though. We...
PR for illustration of possible workflow for adding elements to spatialdata object inspired by https://github.com/scverse/spatialdata/blob/582622f689a7e05421e9d066f98baf702549978f/tests/io/test_readwrite.py#L136 and related to discussion https://github.com/scverse/spatialdata/discussions/520. Currently only implemented for image and labels, but similar approaches...
As @jeffquinn-msk observed, assertions are ignored when the code runs in production. We should verify that no assertion is actually required for the logic of the execution, and in case...
`get_values()` should have an argument, like `index: bool=False`, that should return the index when `index=True`. Returning the index of shapes and points is straighforward, but currently for returning the index...
With the new incremental IO PR we can write single elements or metadata into a Zarr store. However, reading is still a monolithic operation that reads all at once. We...